Why Our Food Keeps Making Us Sick

America’s food industry has a $55.5 billion safety problem.

In the last few months it’s been found in frozen veggies sold at grocery stores like Costco cost, Safeway swy, and Trader Joe’s. Its detection in a manufacturing plant led to the recall of Starbucks’ sbuxbreakfast sandwiches. It’s killed four people who ate packaged salads made by Dole and sent 33 more to the hospital. This is only the tip of the proverbial iceberg. We’re talking about listeria—it’s deadly and, to read the headlines, it would seem the bacteria is everywhere and unstoppable.

In September Fortune dove into the world of food-borne pathogens as we tried to understand what’s making 48 million Americans sick every year. Fortune has resurfaced this story in the wake of the recent string of listeria-related recalls as well as Chipotle’s cmgfood safety crisis, which has become an almost existential threat to the burrito chain. Is there an increasing number of contaminants in our food, or are we just getting better at detecting these outbreaks? Here’s what we found.

Allow us, just for a moment,to be completely—and irresponsibly—alarmist: We are in a battle with bacteria. And from the numbers, it might well appear that we are losing.

Each year an estimated 48 million Americans are stricken ill as the result of one food-borne pathogen or another—listeria, E. coli, salmonella, and even a number of stowaway viruses are among the culprits. But in many cases the victims don’t know they’ve been infected. For those who go to a doctor or the hospital, the collective bill is substantial. A 2015 study by Robert Scharff, an associate professor at Ohio State University, estimates the annual cost of medical treatment, lost productivity, and illness-related mortality at $55.5 billion. For lack of a good Latin name for the constellation of ailments that fall into the above category, we’ll call the pathology “getting sick from what you eat.” And the scariest part is, that’s about as precise as the medical explanation often is. “The route by which most of these individuals get ill is unknown,” says John Besser, the deputy chief of the Enteric Diseases Laboratory Branch at the Centers for Disease Control and Prevention.

That’s not just a scary prospect for those of us who are consuming food these days (that’s you, dear reader), but also for those who are making and selling it. Food-borne illness is a giant, expensive challenge for companies big and small—and the surprise is, their exposure to the risk (and the liability when linked to an outbreak) is arguably bigger than ever. “Thirty years ago if you had a little problem, you were not going to get discovered,” says David Acheson, former associate commissioner for foods at the U.S. Food and Drug Administration, who today runs a consulting firm. “Now the chances of getting caught are significant, and it can be the end of your company.”

Or a costly wound, at the very least. When the Grocery Manufacturers Association surveyed three dozen international companies in 2011, more than half reported being impacted by a food recall during the previous five years. Eighteen percent of those said the hit from the recall and lost sales was between $30 million and $99 million; 5% said the financial impact was $100 million or more. The long-term reputational damage to companies can have an even steeper price tag.

To help solve the problem, in mid-September the FDA released the first set of major rules it was instructed to create by the Food Safety Modernization Act (FSMA), passed long ago in 2011. But honestly, new regs alone won’t solve this problem. Here are four reasons the food-poisoning conundrum is so hard to solve.

1. Health officials can identify only a fraction of those who get food poisoning.

Pinpointing an outbreak of food-borne illness is largely a matter of luck and circumstance. It can take dramatic symptoms for people to visit a doctor, and even then, physicians seldom order a stool sample—the prime way to trace a pathogen to a patient. If a specific germ is found to be the cause, public health authorities may then interview the person to determine what he’s eaten (in the case of listeria, investigators might require a record of food consumption that goes back 28 days). And, well, people forget what they eat. Then epidemiologists have to take this indeterminate recollection of meals and snacks—something that might include hundreds of components—and isolate the source of the culpable microorganism.

None of this is easy. Most cases of food-borne illness are sporadic, meaning they cannot be traced to a specific “outbreak”—an event known to have caused illness in others. Even in the case of an outbreak, it’s woefully hard to identify those who fall ill. For example, out of every 29 people who get sick from a typical salmonella outbreak, the CDC estimates that just one will be formally diagnosed.

Given such long odds, it’s somewhat remarkable how many outbreaks have been isolated in recent years—particularly in cases in which foods and germs were linked together for the first time. For instance, since 2006 investigators have fingered a bacterial strain called E. coli O157:H7 (at one time widely thought to be found only in meats) in bags of baby spinach, in hazelnuts, and in cookie dough. They’ve identified botulism in pasteurized carrot juice and found salmonella in peanut butter, ground pepper, jalapeño peppers, Turkish pine nuts, and pistachios. They’ve discovered hepatitis A virus in pomegranate seeds; cyclospora in bagged salad mix; and Listeria monocytogenes in ice cream. (Read about Blue Bell’s recall crisis here.)

“I’m skeptical that these are new connections,” says Ben Chapman, associate professor of food safety at North Carolina State University, who runs a website called the Barfblog. “It’s stuff that’s always been there, and now we’re looking for it.” That would help explain why FDA-regulated food recalls have more than doubled over the past decade, to 565 last year, according to insurance company Swiss Re—with nearly half related to microbiological contamination. In interviews with more than 30 experts, nearly all said the rise in recalls was less an indicator of deteriorating food safety than it was of our improving capacity to connect the dots between foods and microbes.

2. Regulators have new tools. Industry doesn’t trust them.

Up until the 1990s, most outbreaks we found were in the same geographic location—the church picnic where everyone eats the same bad potato salad and calls in sick the next day. Then new technology enabled scientists to determine the various DNA fingerprints of food-borne bacteria, which were uploaded into a common database. Investigators were suddenly able to link disparate cases of illness by finding bacterial matches. “It revolutionized outbreak investigation,” says Linda Harris, a microbiologist in the department of food science and technology at the University of California at Davis.

Since then the tech has gotten faster and more accurate—a fact that has allowed for the creation of large databases of bacterial genome sequencing. The CDC is building its own library of pathogen genomes isolated from patients. The FDA is doing the same with microbes found in food and company production facilities, a program it calls GenomeTrakr.

Major food companies, meanwhile, commonly test for bacteria in their own food and factories. (Bacteria are everywhere: On each square centimeter of your skin there are potentially millions of the tiny organisms. Worry not—nearly all of them are harmless.) And when companies find any worrisome strains, they increasingly do genetic analyses of their own. It would make sense, certainly, for them to contribute their own data to GenomeTrakr—which is something the FDA strongly encourages. (The word “encourage” here is in the softest sense: Companies are really required to report only contaminations of products that could cause a public health issue.)

But many food manufacturers are wary of giving regulators any information they don’t have to. “There’s clearly a nervousness around it,” says Acheson. “If a company has got data that could incriminate them in an outbreak, they get reluctant to look for it. It’s a very fine line.”

The concern is twofold: First, these techniques are imperfect. Not all genomic sequences of linked food and patient pathogens will have exact matches. “There’s a range of relatedness,” says ­Carlota Medus, an epidemiologist at the Minnesota Department of Health. “The new advancements are more specific,” says Elisabeth Hagen, a former undersecretary for food safety at the U.S. Department of Agriculture who is now a senior adviser to Deloitte. “But there are reasonable questions about what constitutes a match and how the technology will be used to definitively identify the source of an outbreak.”

The second worry is that regulators will shoot first and ask questions later. Companies fear they will be implicated before the necessary epidemiology is done. “They could send a swat team into a plant, and the business is going to be disrupted significantly,” says Mike Robach, vice president of corporate food safety, quality, and regulatory affairs at ­Cargill. “We just want to make sure we have due process and are not falsely accused.”

One potential solution is VoluntaryNet, which is run by Michael Doyle at the University of Georgia’s Center for Food Safety. Currently Cargill and other companies anonymously submit bacteria samples that might cause food-borne illness to Doyle’s team, which genetically sequences them. If the university researchers discover a match with a genetic isolate from a patient in the CDC database, they send a report to all the food companies in the network, letting them know of a potential contamination link.

3. Our pantry is global. (So are the chances for contamination.)

Americans love strawberries—we annually consume about eight pounds of them per capita—and we want them year round. The berries we can’t get from U.S. growers we bring in from Mexico, mostly. Overall we import nearly 20% of our food—and each of these exporting countries has different food-safety standards and inspection regimes.

The global supply chain has not only given us a cornucopia of food choices; it has also cut costs. The downside is that it has made preventing food-borne contamination nearly impossible. By the time milk tainted with melamine produced in China was detected, it had already been exported to 47 countries by way of milk-containing products.

The more stops food takes before it enters the U.S., the more opportunities there are for contamination, says Bill Marler, an attorney and an oft-cited authority on food-borne illness. Companies now fret about so-called economic adulteration, in which suppliers in some cases add something to food that shouldn’t be there—as occurred with the melamine scandal in China, when the chemical was put in diluted milk to increase its protein content. This form of food fraud—which happens most prevalently in liquids like olive oil and in powders such as spices—costs the industry $10 billion to $15 billion a year. “I’m not sure we truly worried about this 20 years ago,” says Sara Mortimore, vice president of product safety, quality, and regulatory affairs at Land O’Lakes. And for companies, the stakes could get much higher: Additional FSMA rules anticipated later this year are expected to hold importers responsible for whatever they bring into the country.

4. Oh, yeah—and it’s our fault too.

Increasingly, consumers are rebelling against preservatives—fearing those additives intended to prevent food poisoning more than the sickness itself (see our special report, “The War on Big Food,” on Fortune.com). Cargill’s Robach says a number of customers have asked the company to remove the potassium and sodium lactates and diacetates it puts in processed meat to inhibit listeria growth. “We have not taken it out because we feel there’s an added layer of protection that’s important,” he says.

A growing segment is also pressuring manufacturers to cut back on salt and sugar—both of which help prevent bacterial growth by reducing the amount of available water in food that the microbes can grow in. Then there’s freezing, which also boosts food safety. But today’s shoppers are turning away from frozen food because of a desire for fresh goods, which they equate with healthy.

Some food companies are experimenting with techniques like high-pressure processing, which squashes the bacteria on the surface. But it can impact quality. “You can’t do that with a tomato,” says Acheson. A similar concern is voiced over food irradiation, which is even more off-putting to many than sugar, salt, and preservatives.

Ironically, trying to eat more fruit and vegetables—especially raw—can be the riskiest thing of all. We eat them without performing what food-­industry vets call a “pathogen-reduction step.” Most of the rest of us call it cooking.

Is there a solution?

Pizza is perhaps the best example of why our regulatory structure is a challenge. “It’s very confusing,” says Secretary of Agriculture Tom Vilsack, who visited Fortune in mid-September. “If it’s a plain pizza with tomato sauce, mozzarella, crust, it’s the FDA. If it’s a slice of pepperoni, it’s mine. Sausage, it’s mine. Mushroom, it’s theirs.” Indeed, it is hard to conceive of a more haphazard regulatory regime than the one intended to protect Americans’ food. The USDA regulates meat, poultry, and processed egg products and has an agent in every processing plant in the U.S. The FDA minds everything else but requires no testing of food from manufacturers. That’s not to suggest that testing is the obvious cure-all for our seemingly endemic food-safety predicament. “If you take a whole bunch of lettuce heads off a truck and test one out of 100, you still might not find a problem because it’s not likely to be spread evenly,” says North Carolina State’s Chapman. “We could have a really big sampling program and never find a pathogen.”

That’s why regulators—and companies—are focusing more on prevention. The new FSMA rules, indeed, mark a big regulatory shift: one that mandates companies take a more proactive approach to food safety rather than wait for an outbreak to trigger a frantic cleanup response. “Instead of the FDA having to show that firms are doing something wrong, firms have to show that they’re doing something right,” says Charles Breen, a former FDA district director who is now a food-safety consultant.

As for consumers (again, that’s you): Use a meat thermometer, wash your hands, don’t drink raw milk. Those in the know also suggest being especially wary of items like oysters, sushi, and sprouts. Bill Marler, for one, routinely chucks the bagged salad that his wife buys. “I will grab it out of the refrigerator and throw it away,” he says. What’s the safest thing to eat? That’s easy, he says. Scotch.